This tutorial will guide you to create cohorts in Garibaldi’s paper using ATLAS
Patient Trajectories Among Persons Hospitalized for COVID-19 A Cohort Study https://www.acpjournals.org/doi/10.7326/M20-3905
cohort as a set of persons who satisfy one or more inclusion criteria for a duration of time. The term cohort is often interchanged with the term phenotype. riation in the data while also allowing for identification of potentially missing values. —Book of OHDSI Chapter 10 Define Cohorts
When creating a cohort definition, you need to ask yourself the following questions:
The standard components we use to assemble these criteria are:
Domain : The CDM domain(s) where the data are stored (e.g. “Procedure Occurrence”, “Drug Exposure”) define the type of clinical information and the allowable concepts that can be represented inside that CDM table. Domains are discussed in more detail in Section 4.2.4.
Concept set: A data-agnostic expression that defines one or more Standard Concepts encompassing the clinical entity of interest. These concept sets are interoperable across different observational health data as they represent the standard terms the clinical entity maps to in the Vocabulary. Concept sets are discussed in Section 10.3.
Domain-specific attribute: Additional attributes related to the clinical entity of interest (E.g. DAYS_SUPPLY for a DRUG_EXPOSURE, or VALUE_AS_NUMBER or RANGE_HIGH for a MEASUREMENT.)
Temporal logic: The time intervals within which the relationship between an inclusion criteria and an event is evaluated (E.g. Indicated condition must occur during 365 days prior to or on exposure start.)
exampleLogical Diagram of Intended Cohort- Hyptertension
Patients: 832 consecutive COVID-19 admissions from 4 March to 24 April 2020, with follow-up through 27 June 2020.
Definitions of cohorts used in Garibaldi’s paper
What concept sets do we need ?
1. Inpatient
2. SARS Covid-19 test (Concepts udner measurement domain)
3. Suspected SARS (concepts under Observation domain)
4. Severity groups concept sets based on WHO scale
Create new concept set.1
Create new concept set.2
Create new concept set.3
Follow the WHO scale logic create concept sets:
WHO scale
* score 5- concepts of high flow nasal cannula (device domain) & noninvasive ventilation (procedure domain)
* score 6- concepts of intubation and mechanical ventilation ( device and procedure domain)
* score 7- ECMO & ivpressor & hemodialysis (device and procedure domain)
Cohorts sets will be used:
#60 inpatient
#18 SARS Covid-19 test
#30 suspected SARS
#21 [annals]Severe-WHO score 5 High Flow Oxygen & Nippv
#23 [annals]Severe-WHO score 6 intubation & mechanial ventilation
#68 [annals]Severe-WHO score 7 ivpressor & ECMO & hemodialysis
Create new cohort.1
Create new cohort.2
Create new cohort.3
Create new cohort.4
Create new cohort.5
Note: Value as concept is positive ( concept_id=45884084), negative (concept_id=45878583)
Here we used LONIC code
We need to define:
study cohorts and mild/severe/death patient cohorts for characteriztaions and incidence rates analysis
Create new cohort.6
Load exist definition
WHO scale score 8
WHO scale score 5-7
Check the graphical definition under Cohort Definitions->select one cohort -> Export -> Graphical View
graphical logic of inclusion criteria
Patients without exposure to any device/procedure in WHO scoree 5-8 concept sets are in the goupr WHO score 3-4.
Create cohort
1.Copy cohort [outcome][Annals paper]Hospitalized Patient with SARS positive results between 2020/03/04-2020/04/24-WHO score 5-7.
2. Change new cohort’ name and save.
3. Change inclusion criteria for WHO score 5-7: exclude patients dead or had any procedure and device exposure of WHO score 5-7 criteria.
WHO scale score 3-4 inclusion critreria design
Graphical logic of WHO score 3-4 inclusion criteria
event cohorts